change output in create html

create_html.py

@@ -202,7 +202,7 @@ def main():
             if opt in ("-t"):
                 tsvfile = arg
             elif opt in ("-o"):
-                sys.stdout = open(arg, 'w')
+                outputfile = arg
     except getopt.GetoptError:
         print("please use this command as follow: ")
         print('usage : python2.7 create_html.py -v <vcf/file> -h <report/from/HLAscan> -t tableau_pharmgkb.tsv -o <path/to/file/results>')
@@ -222,6 +222,10 @@ def main():
         print('No tsv file given')
         print('usage : python2.7 create_html.py -v <vcf/file> -h <report/from/HLAscan>  -t tableau_pharmgkb.tsv -o <path/to/file/results>')
         sys.exit(1)
+    if not vars().has_key('outputfile'):
+        print('No output file given')
+        print('usage : python2.7 create_html.py -v <vcf/file> -h <report/from/HLAscan>  -t tableau_pharmgkb.tsv -o <path/to/file/results>')
+        sys.exit(1)
 
     # Check files
     try:
@@ -242,6 +246,12 @@ def main():
     except IOError:
         print('PharmGKB tsv file does not exist')
         sys.exit(1)
+    try:
+        f = open(outputfile, 'w')
+        f.close()
+    except IOError:
+        print("Can't open output file" )
+        sys.exit(1)
 
     #execute
 
@@ -251,7 +261,8 @@ def main():
     body=extract_rs(tsvfile,vcfSNP,DictRs,body)
     body=extract_HLA(report,DictHLA,body)
     
-    print(htmltag.HTML(head+body))
+    with open(outputfile,'w') as output:
+        output.write(htmltag.HTML(head+body))
 
 if __name__ == "__main__":
     main()
\ No newline at end of file